The Shrimps, who are still in with a firm shout of lifting themselves into the play-off places, were by far the better side as Boro face an uphill fight next year if they are to keep their Conference National status.
During a bright opening, Farnborough were the first to create with Gary Holloway weaving his way across the midfield before unleashing a shot from the right channel that bobbled wide in the sixth minute.
The visitors responded with Danny Carlton drilling a right-footed shot against Craig Holloway's crossbar five minutes later before the same player fired them ahead with a well-struck shot inside the box after 12 minutes.
The goal gave Morecambe the sharpness they would have been looking for and Harvey's side continued to keep possession well with strikers Wayne Curtis and Carlton looking a constant threat.
The home side's first attempt on target came in the 42nd minute with Ryan Robinson saving easily from a Nick Burton header.
Morecambe nearly doubled their advantage in the 43rd minute though with Carlton setting up Gary Thompson, before Craig Holloway saved well and Danny Allen-Page cleared the danger.
However, before the break they went further ahead with Curtis collecting Lee Elam's centre and picking his spot past Craig Holloway despite the keeper getting a good hand on the ball.
In the second half, Morecambe continued to stay on top but the game heated up considerably in the bitter Christmas cold 18 minutes after the restart.
Stephen Hughes, who worked hard for the home side, went in over the top and late on Shrimps skipper David Perkins.
The Boro striker earned a yellow card for the challenge but defender Chris Blackburn was then sent off in the melee that resulted for throwing the ball at the main culprit Hughes.
Substitute Richard Pacquette, who had replaced Harkness in the 70th minute, hauled Boro back into the contest nine minutes after his introduction, hitting into an empty net after Ali Chaaban's strike had been parried into his path.
Playing against 10 men, Boro briefly had their tails up but there wasn't enough in the tank to deny an impressive Morecambe outfit who were worthy winners.